BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013284.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,410,828 number of mapped reads = 2,011,172 (83.42%) number of supplementary alignments = 18,276 (0.76%) number of secondary alignments = 0 number of mapped bases = 125,507,720 bp number of sequenced bases = 125,445,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 224,755 duplication rate = 8.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.735 >>>>>>> ACTG content number of A's = 36,203,238 bp (28.86%) number of C's = 23,593,332 bp (18.81%) number of T's = 38,546,200 bp (30.73%) number of G's = 27,059,771 bp (21.57%) number of N's = 43,340 bp (0.03%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,073,555 number of insertions = 8,332 mapped reads with insertion percentage = 0.41% number of deletions = 36,456 mapped reads with deletion percentage = 1.79% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.4307X There is a 2.21% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7660993 0.03073610396340798 0.6839318304861424 chr2 243199373 11413235 0.04692954122048662 0.4233233979517945 chr3 198022430 10347369 0.052253519967409755 0.3873754437232473 chr4 191154276 10686687 0.05590608394237542 0.39411449619606786 chr5 180915260 4877154 0.026958223424602214 0.26752670975084675 chr6 171115067 9195990 0.053741556259332794 0.42535443778747856 chr7 159138663 6095313 0.038301899017462525 0.5008632048981975 chr8 146364022 4598177 0.03141603337464995 0.6538967936434635 chr9 141213431 3817879 0.02703623141909214 0.3050481793284734 chr10 135534747 8256580 0.06091854806797256 0.5074789947072631 chr11 135006516 3653778 0.027063715946865855 0.29528859308934 chr12 133851895 5378653 0.04018361488270301 0.3290162070365631 chr13 115169878 3543613 0.030768574748338277 0.286995096453145 chr14 107349540 8106931 0.07551901014200899 0.4619629511980788 chr15 102531392 2615778 0.02551197198220034 0.266335252880137 chr16 90354753 5669351 0.062745465089147 0.40670732739543525 chr17 81195210 4650376 0.05727401899693344 0.3911384454984951 chr18 78077248 1694506 0.02170294219386421 0.47563737019629726 chr19 59128983 3141917 0.05313666565176675 0.5681072127428077 chr20 63025520 2337495 0.03708807162558913 0.3203716799045713 chr21 48129895 1734994 0.0360481567641068 0.30541078528602456 chr22 51304566 855845 0.016681653636832248 0.26998985618208554 chrMT 16571 12603 0.7605455313499487 1.2795736918224332 chrX 155270560 4932708 0.031768469180506596 0.30178762797295444 chrY 59373566 229795 0.003870325053408448 0.0912783588253584